(Bcftools) SNP allele frequency in DNA pools

I tried to use Bcftools to calculate allele frequency by SNP variants after bowtie 2 alignment.

 bcftools mpilup --redo-BAQ --min-BQ 30 --per-sample-mF --annotate FORMAT/AD, FORMAT/ADF, FORMAT/ADR,FORMAT/DP,FORMAT/SP,INFO/AD,INFO/ADF,INFO/ADR -F reference.faa.txt reads-sorted.bam } bcftools call --multiallelic-caller --variants0only -0v > new.vcf

And after +fill-tags for AF, I used query to calculate AF for me. However, all position show AF: 0.5? I am confused how to calculate SNP allele frequency estimation in DNA pools.

snp

• 1,205 views • link

updated 3.1 years ago by Ram

• written 6.0 years ago by gwyneth0011 •

0 answers

No answers yet.

More posts like this

Filtering of tricky overlapping sites in VCF
written 3.4 years ago by dr_cfoster

I'm working on a project where I'm working with variants ranging from low frequency (AF~=0.03) up to high frequency (AF=1) after variant calling with `lofreq`. …
Bcftools how to add SNP type to the INFO field (DEL,INS,INV,DUP..)
written 4.4 years ago by Michal Nevo •

Hi, I have a VCF file [Which I created with bcftools mpileup| bcftools call ] and I want to make sure that the Bcftools stats …
Pooled-heterozigosity (SECTION2)
written 4.7 years ago by reza

Following the [question][1] I asked before and unfortunately did not receive any help, I have another question that I hope will benefit from your help. …
How to correctly calculate Alternative Allele Frequency (AAF) from Samtools mpileup
written 4.8 years ago by Daniel •

I have a hard time to figure it out how correctly calculate the `Alternative Allele Frequency (AAF)` from `Samtools mpileup`. I received the code which …
bcftools call error "--gvcf output mode requires FORMAT/DP tag, which is not present in the input h…
written 6.9 years ago by AGE •

I would like to get non-variant sites using bcftools but am getting an odd error about the DP field. bcftools mpileup -f genomic.fa file.bam | …
How to set up my vcf with a minimum depth?
written 7.1 years ago by apl00028

I am trying to set up the minimum depth which samtools mpileup considers a polymorphism for RNAseq samples. For that I did this: I did …
How can I detect low frequent polymorphisms ?
written 7.1 years ago by apl00028

Hi everybody, I am trying to detect polymorphisms (and their proportions) to sanger sequences of the genes that codify for Watermelon Mosaic Virus Coat protein: …
How can I see the low frequency SNP
written 7.3 years ago by apl00028

I have created a vcf file from bam file using bcftools: bcftools mpileup \ --redo-BAQ \ --min-BQ 30 \ --per-sample-mF \ --annotate \ FORMAT/AD,FORMAT/DP,INFO/AD -f …
Estimating cross contamination in a set of BAMS
written 8.1 years ago by Pierre Lindenbaum

Hi all, I've received a set of BAM files , the variant were called with bcftools ${bcftools_exe} mpileup -Ou -f "${REF}" \ --bam-list "${bam_list}" \ …
How can I add PV4 or BQ or NS to my VCF file
written 8.7 years ago by sahar.voghoei •

I am trying to extract maximum features for my machine learning input, and I need PV4, BQ, G3, NS to be added to my VCF …